; Technologies, applications and data analysis Course 2542 Dr. Martie C.M. Verschuren Research group Analysis techniques in Life Science, Breda Prof. dr. Johan T. den Dunnen Leiden Genome Technology Center, Human and clinical Genetics, LUMC, Leiden 27-29 March 2012 Research Group Analysis Techniques in Life Science P.O. Box 90116 4800 RA Breda The Netherlands www.alsavans.nl All rights reserved. No part of this publication may be reproduced or transmitted, in any form or by any means, without permission from Breda
Code 2542 Tuesday March 27, 2012 Next generation sequencing technologies 09.00 Arrival, registration, coffee, and general introduction [2] (Dr. Martie Verschuren, ) 09.30 Overview NGS: General terminology [3] (Dr. Henk Buermans, LUMC, Leiden) 09.50 Lecture: Roche / 454 technology and Ion Torrent platforms [4] (Ing. Marja Jakobs, AMC Amsterdam) 10.40 Coffee/Tea 10.55 Lecture: Illumina / Solexa technology platform [5] (Ing. Yavuz Ariyurek, LUMC, Leiden) 11.45 Lecture: ABI / SOLID technology platform [6] (Dr. Ies Nijman, Hubrecht laboratory, Utrecht) 12.35 Lunch Next generation sequencing applications 13.30 Lecture: ChIP-seq [7] (Dr.Wilfred van IJcken, Erasmus MC, Rotterdam) 14.15 Lecture: RNA expression profiling [8] (Peter-Bram t Hoen, LUMC, Leiden) 15.00 Lecture: mirna profiling [9] (Dr. Henk Buermans, LUMC, Leiden) 15.45 Coffee/Thee 16.00 Computer practical, parallel sessions with Genome browser views on: ChIP-seq, RNApressio0n profiling and mirna profiling 18.00 End of the course day one.
Code 2542 Wednesday March 28, 2012 Next generation sequencing applications 09.00 Welcome coffee and introduction of day 2 09.30 Lecture: Re-sequencing and SNP discovery [10] (Dr. Hendrik-Jan Megens, WUR, Wageningen) 10.15 Lecture: Paired end mapping [11] (Dr. Victor Guryev, Hubrecht laboratory, Utrecht) 10.45 Coffee/Thee 11.00 Lecture: targeted Sequencing[12] (Dr. Marjolein Kriek, LUMC, Leiden) 11.45 Computer practical, parallel sessions with Genome browser views on: Re-sequencing, Hyb capture, and Paired end mapping 13.00 Lunch 14.00 Lecture: De novo sequencing : a tool to discover novel pathways in microorganisms [17] (Huub Op den Camp, IWWR, Radboud University Nijmegen) Next generation sequencing data analysis 14.45 Lecture: Introduction to Nextgene data analysis [14] (Robert Akkers, Bioke) 15.15 Coffee/Thee 15.30 Computer practical: Windows practical: Nextgene data analysis (Robert Akkers, Bioke) 17.30 The end of day two.
Code 2542 Thursday March 29, 2012 Next generation sequencing data analysis 09.00 Welcome coffee and introduction day 3 09.30 Lecture: Metagenomics [15] (Dr. Sacha van Hijum, Nijmegen) 10.15 lecture: Introduction to CLCbio data analysis [16] (Patrick Dekker, CLCbio) 10.45 Coffee/Thee 11.00 Computer practical: Windows practical: CLCbio Workbench (Patrick Dekker, CLCbio) 13.00 Lunch 14.00 Lecture: Targeted resequencing of oncogenes for mutation and copy number variation analysis [13] (Dr. Peter Verhasselt, Johnson and Johnson, Belgium) 14.45 Future developments and single molecule sequencing (Helicos) [18] (Prof.dr. Johan den Dunnen, LUMC, Leiden) 15.30 General discussion (Prof.dr. Johan den Dunnen, LUMC, Leiden) 16.30 Evaluation and official closing of the course 17.00 End of the course reserves the right to modify course materials or substitute speakers without notice.
; Data analysis Pipelines Course 2542b Dr. Martie C.M. Verschuren Research group Analysis techniques in Life Science, Breda Prof. dr. Johan T. den Dunnen Leiden Genome Technology Center, Human and clinical Genetics, LUMC, Leiden March 30, 2012 Research Group Analysis Techniques in Life Science P.O. Box 90116 4800 RA Breda The Netherlands All rights reserved. No part of this publication may be reproduced or transmitted, in any form or by any means, without permission from Breda
Code 2542b Friday March 30, 2012 EXTRA DAY Data analysis pipelines 09.00 General Introduction [3] 09.20 Lecture: Introduction to Linux [4] 09:40 Lecture: Command line and NGS tools [5] (Ing. Michiel van Galen, LGTC, Leiden) 10.10 Coffee/Thee 10:40 Lecture: Connecting to other machines [6] 11.10 Computer practical 1, General tools used in NGS: Command line practice. Splitting on bar codes. Alignment and SNP calling. (Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden) 12.00 Lunch 13.00 Lecture: NGS Pipelines [7] (Ing. Michiel van Galen, LGTC, Leiden) 13.30 Lecture: Galaxy and GAPSS [8] 14.00 Break 14.30 Computer practical 2, pipelines for complete analysis: Variant calling Expression analysis (CAGE). (Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden) 15.30 Questions and Discussion 16.00 End of the course reserves the right to modify course materials or substitute speakers without notice.